The streamflow is solely from the chlorinated effluent released from a tertiary treated wastewater. Finally this stream is merged to another river and flow speed of the river is decreasing from initial discharge point to downstream.
Other sources of BOD may be possible as non point pollution from animals, organic materials, stormwater runoff, etc. You may want to evaluate all the land uses with potential non point pollution sources or potential, and test all the tributaries contributing to the lower sampling point.
Keeping in mind that BOD is biochemical oxygen demand, i.e. how much oxygen is consumed buy natural bacteria in the water, and that your water is chlorinated, it could be the case that the chlorine is disturbing the bacteria which activity you measure. As the water flow downstream chlorine is diluted and evaporating and the bacteria are more active.
To test this hypothesis test COD upstream and downstream or neutralize the chlorine in the upstream and test BOD again.
Also see this quote "Chlorine can also affect BOD measurement by inhibiting or killing the microorganisms that decompose the organic and inorganic matter in a sample. If you are sampling in chlorinated waters, such as those below the effluent from a sewage treatment plant, it is necessary to neutralize the chlorine with sodium thiosulfate. (See APHA, 1992.)"
https://archive.epa.gov/water/archive/web/html/vms52.html
But its even more complex, short chlorination may increase BOD by modification of the organic compounds...
https://www.sciencedirect.com/science/article/pii/004313549400234X
Bottom line, chlorination can effect your BOD (and COD) - both ways...
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